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```python
import cogent3
import pprint
aln = cogent3.load_aligned_seqs("https://github.com/user-attachments/files/17796702/example.phy.gz", format="phylip", moltype="dna")
phylo_gtr = cogent3.ge…
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(running on a fresh ubuntu-server-24-04, with Miniconda3)
``` text
/home/fred/NanoASV/workflow/run.sh: line 252: [: missing `]'
Checking reference format
/home/fred/NanoASV/workflow/snakefile:200: Sy…
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## Add probability column to input dataframe
Probability column can also be a p-value.
Probabilistic edge (connected to a node with multiple parents) should be different in colour or line type compa…
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This is the validation dataset.
```
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/pathogensurveillance] Pipeline completed with errors-
ERROR ~ Error executing process > 'PATH…
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**Describe the bug**
Clamping a variable causes it to be omitted from log files.
**To Reproduce**
- Download [data.txt](https://github.com/user-attachments/files/17519572/data.txt)
```rb
se…
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Probably a simple approach to visually compare the backbones of the Viridian UShER tree and our pandemic-scale ARG is to leverage the Pango lineage roots, excluding the Pango recombinants. The Pango l…
szhan updated
1 month ago
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Feature request via WA-DoH (via [slack](https://bedfordlab.slack.com/archives/C01G4B4UY31/p1730391930819899)): annotating mutations between the inferred root and the reference sequence is necessary fo…
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**Describe the bug**
`model.graph()` causes a segmentation fault when tracking `dnPhyloCTMC(coding = variable).lnProbability()`
**To Reproduce**
- Download [data.txt](https://github.com/user-a…
ms609 updated
2 weeks ago
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Currently, the package does not allow `multiPhylo` tree objects with different numbers of internal nodes. This is potentially an issue, as this excludes valid trees with polytomies where three or more…
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@fercol
I am reanalysing the post-2005 data, which has a slightly different format from the older one - that is fine. I will figure this out and adapt the code accordingly.
Yes, I found out tha…